chore(scripts): read tooling configuration with tomllib

[yeongseon]

Summary

Read pyproject.toml through Python 3.11's tomllib in scripts/check_tool_versions.py. Dependency groups, published extras, Ruff scope and Python classifiers now use parsed TOML data. Exact Ruff/Mypy pin validation accepts requirement extras and still rejects missing, ranged or duplicate declarations. Other tooling checks are unchanged.

Scope

Only scripts/check_tool_versions.py and test/test_tool_versions.py change. The tests cover valid TOML formatting, extras, duplicate and ranged pins, missing or incorrectly typed dependency groups, unbounded Alembic requirements, valid dependency-group includes, and the existing drift checks. Exact pin tests now derive their versions from the current configuration. This PR has no file overlap with open PRs #811 and #812.

Validation

• pytest --noconftest test/test_tool_versions.py -q -k 'not active_environment_agree': 30 passed, 1 deselected.
• ruff check scripts/check_tool_versions.py test/test_tool_versions.py: passed.
• ruff format --check scripts/check_tool_versions.py test/test_tool_versions.py: passed.
• python3.11 -c 'from pathlib import Path; from scripts.check_tool_versions import check, declared_pins; print(declared_pins(Path.cwd())); print(check(Path.cwd()))': returned the current pins and [].
• git diff --check: passed.
• Full pytest test/ -m repo could not start locally because SQLAlchemy is not installed; creating a fresh environment was blocked by a PyPI connection error. The direct CLI ran and reported the host's existing Ruff/Mypy versions differ from the repository pins. CI must provide the full repo-test and pinned-environment evidence.

Docs: not needed - this changes only an internal developer-tool parser and preserves the existing configuration policy and public behavior.

Closes #763

[Copilot]

🟡 Changes recommended

Exact pins with valid whitespace are rejected, and several tests remain coupled to current pin versions.

2 open findings

• Trim whitespace around exact pin names and versions · New
• Base pin replacements on currently declared versions · New

What changed in this PR

Replaces regex-based pyproject.toml inspection with structured tomllib parsing for repository tooling checks.

Changes:

• Parses dependency groups, extras, Ruff scope, and classifiers structurally.
• Adds exact-pin validation supporting requirement extras.
• Expands parser and invalid-configuration tests.

File	Description
scripts/​check_tool_versions.py	Implements TOML-based tooling validation.
test/​test_tool_versions.py	Adds parser and pin-validation coverage.

🧠 Review effort: Balanced

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[yeongseon]

Review status: complete for head 1807c50.

Development route: standalone Codex. Copilot submitted a substantive COMMENTED review on 38b0a90; both findings were fixed in 780357f and 3408b38, checked at the final head, and their inline threads are resolved. A separate Codex review identified a valid dependency-group include regression; 1807c50 fixes it with a focused test. An independent final-head review found no actionable regression.

Local focused validation: 30 passed, 1 environment-dependent test deselected; Ruff check and format, direct configuration check and diff check passed. Final-head PR CI is green, including repo-tests, integration, matrix-result, lint, typecheck and security checks. The full repository test command and pinned-tool environment check did not run locally because dependencies could not be installed; CI supplied the required repository-test evidence. No blocking findings or unresolved threads remain.